<br><br><div class="gmail_quote">On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word"><div><br></div>Really? This is really great! <div>Is there any need to specify the location of the vmd libraries? </div></div></blockquote><div>By default it tries to find them at</div><div>
/usr/local/lib/vmd/plugins/*/molfile</div><div><br></div><div>If you have them installed somewhere else you can specify it by setting the VMD_PLUGIN_PATH environment variable.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word"><div>If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this </div><div>somehow still possible? </div></div></blockquote><div>It would be pretty simple to add, that one can read this molecule information also from pdb or from psf. But I didn't have time to do it. In case you are interested to do that, I can give you help doing it.</div>
<div><br></div><div>Until someone implements it, one still needs the tpr file. For cases where it is difficult to generate a top file we have a version of psfgen which generates a top file from a psf. But we don't have solved the license issue so far (NAMD license) and thus can't provide this version yet.</div>
<div><br></div><div>Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word"><div><div></div><div class="h5"><div><br>
<div><div>On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote:</div><br><blockquote type="cite">In case you use the GIT version of the analysis tools you don't need to convert the trajectories first.<div>I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries.</div>
<div><br></div><div>Roland<br><br><div class="gmail_quote">On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br> Well I guess you want to use gmx analysis tools so you'll have to<br> build the gmx topology of your system when necessary! Often<br>
only a pdb file or a gro file is sufficient.<div><div></div><div><br> <br> On Apr 16, 2010, at 5:24 PM, ram bio wrote:<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks Xavier,<br> <br> Could you make it more eloborate...<br> <br> Ram<br> <br> On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br> VMD reads Desmond trajectories and writes GMX format ...<br> Rests the topology to deal with ...<br> <br> On Apr 16, 2010, at 4:15 PM, ram bio wrote:<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All,<br> <br> I have run a dynamics of protein ligand complex in lipid bilayer dppc<br> using desmond software and would like to convert the trajectory files<br> files into gromacs format, is it possible?? if so, please let me know<br>
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